[2024-01-24 12:37:24,754] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,756] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4046df9-4ed4-48c2-8fa9-748dd3a69294/dqc_reference
[2024-01-24 12:37:26,158] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,159] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e9fffff-32f2-4f03-a204-0e29ca4540bf/GCF_014203125.1_ASM1420312v1_genomic.fna.gz | prodigal -d GCF_014203125.1_ASM1420312v1_genomic.fna/cds.fna -a GCF_014203125.1_ASM1420312v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:41,097] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:41,098] [INFO] Task started: HMMsearch
[2024-01-24 12:37:41,098] [INFO] Running command: hmmsearch --tblout GCF_014203125.1_ASM1420312v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4046df9-4ed4-48c2-8fa9-748dd3a69294/dqc_reference/reference_markers.hmm GCF_014203125.1_ASM1420312v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:41,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:41,393] [INFO] Found 6/6 markers.
[2024-01-24 12:37:41,438] [INFO] Query marker FASTA was written to GCF_014203125.1_ASM1420312v1_genomic.fna/markers.fasta
[2024-01-24 12:37:41,439] [INFO] Task started: Blastn
[2024-01-24 12:37:41,439] [INFO] Running command: blastn -query GCF_014203125.1_ASM1420312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4046df9-4ed4-48c2-8fa9-748dd3a69294/dqc_reference/reference_markers.fasta -out GCF_014203125.1_ASM1420312v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:42,396] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:42,398] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:42,399] [INFO] Target genome list was writen to GCF_014203125.1_ASM1420312v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:42,411] [INFO] Task started: fastANI
[2024-01-24 12:37:42,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e9fffff-32f2-4f03-a204-0e29ca4540bf/GCF_014203125.1_ASM1420312v1_genomic.fna.gz --refList GCF_014203125.1_ASM1420312v1_genomic.fna/target_genomes.txt --output GCF_014203125.1_ASM1420312v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:09,280] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:09,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4046df9-4ed4-48c2-8fa9-748dd3a69294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:09,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4046df9-4ed4-48c2-8fa9-748dd3a69294/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:09,298] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:09,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:09,299] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	100.0	1685	1691	95	conclusive
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	83.1594	996	1691	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	82.9352	1014	1691	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	82.8858	1020	1691	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	82.792	921	1691	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	82.0213	879	1691	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	81.4062	875	1691	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	81.3633	855	1691	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	81.3241	927	1691	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	81.0572	857	1691	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	80.9929	869	1691	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	80.9762	904	1691	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	80.9255	874	1691	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	80.9246	856	1691	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	80.9224	888	1691	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	80.8016	861	1691	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	80.6816	902	1691	95	below_threshold
Afipia birgiae	strain=34632	GCA_000308295.2	151414	151414	type	True	79.486	674	1691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:09,301] [INFO] DFAST Taxonomy check result was written to GCF_014203125.1_ASM1420312v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:09,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:09,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:09,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4046df9-4ed4-48c2-8fa9-748dd3a69294/dqc_reference/checkm_data
[2024-01-24 12:38:09,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:09,360] [INFO] Task started: CheckM
[2024-01-24 12:38:09,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203125.1_ASM1420312v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203125.1_ASM1420312v1_genomic.fna/checkm_input GCF_014203125.1_ASM1420312v1_genomic.fna/checkm_result
[2024-01-24 12:38:54,177] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:54,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:54,208] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:54,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:54,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203125.1_ASM1420312v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:54,209] [INFO] Task started: Blastn
[2024-01-24 12:38:54,209] [INFO] Running command: blastn -query GCF_014203125.1_ASM1420312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4046df9-4ed4-48c2-8fa9-748dd3a69294/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203125.1_ASM1420312v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:55,964] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:55,970] [INFO] Selected 9 target genomes.
[2024-01-24 12:38:55,970] [INFO] Target genome list was writen to GCF_014203125.1_ASM1420312v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:55,977] [INFO] Task started: fastANI
[2024-01-24 12:38:55,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e9fffff-32f2-4f03-a204-0e29ca4540bf/GCF_014203125.1_ASM1420312v1_genomic.fna.gz --refList GCF_014203125.1_ASM1420312v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203125.1_ASM1420312v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:10,227] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:10,236] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:10,236] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014203125.1	s__Rhodopseudomonas rhenobacensis	100.0	1685	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000013745.1	s__Rhodopseudomonas palustris_D	91.2117	1343	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014825.1	s__Rhodopseudomonas palustris_B	84.7539	1150	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377015.1	s__Rhodopseudomonas sp013377015	84.0421	1005	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215605.1	s__Rhodopseudomonas palustris_L	83.7137	1056	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935205.1	s__Rhodopseudomonas palustris_E	83.6777	908	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013365.1	s__Rhodopseudomonas palustris_J	83.5842	1044	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217325.1	s__Rhodopseudomonas faecalis	82.7715	924	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.30	98.30	0.93	0.93	2	-
GCF_010907035.1	s__Rhodopseudomonas sp010907035	82.4828	978	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:10,239] [INFO] GTDB search result was written to GCF_014203125.1_ASM1420312v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:10,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:10,243] [INFO] DFAST_QC result json was written to GCF_014203125.1_ASM1420312v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:10,243] [INFO] DFAST_QC completed!
[2024-01-24 12:39:10,243] [INFO] Total running time: 0h1m45s